Excluding wp-mail(in code) from using new email template

Is there a way to exclude wp-mail() function from using the overridden email templates.

e.g WordPress should use the template override for email set by your plugins for its default mail only…but when wp-mail() is individually used in code …it should NOT use the new template (overridden by your plugin) but rather use normal wordpress template

You have all of that a bit backwards – WP Email Template does not send any emails – It applies the email template to all mail sent via wp-mail which is the default mail function of WordPress.

If a plugin sends mail via anything other than wp-mail the template is not applied, if it uses the default wp-mail of WordPress it is applied – UNLESS you use the plugins options to exclude that email from having the template applied.